Why couldn't you just use a modifier key for LtRs? Chivalry uses the ALT key with LMB to queue LtR attacks, the same could be done here with the addition of allowing you to rebind it. This seems to follow suit with the coming combat maneuvers such as thrusts, draw cuts, pulls (think of hooked weapons) and even thaumaturgy. All these will inevitably require some additional input to pull off, but not everyone has a mouse with extra keys. The only sure fire way, imo, to address this input for all players is to keep them on the keyboard. Should you be able to rebind them in the future, that is your own right and you should do it in a way that makes sense to 'you'. For myself, I run in and out of combat with RMB. This feels very natural and I never have to think about what RMB might do in this situation.
As for attack directions, I believe this is sorta intrinsic to the system. Every weapon already behaves differently and you need to actually practice if you want to succeed. They each offer different strengths, weaknesses, and strategies that you really can't understand without putting some time and understanding in. This, imo, is incredibly deep and any player can hone unique skills that are completely there own. I do agree that a certain increase in control may benefit this depth but as it stands now (beta!), it is immensely rewarding and satisfying. I think the coming update will address a least some concerns with inconsistencies in the attack patterns but in the end, it comes down to 'your' play/inputs.
I feel your pain on those LtRs going a little high. I've always felt it came down to how fast I pivoted my body with the swing. A LtR while standing still seems to hit the chest pretty consistently. However, if I'm in the groove, I go pretty much all out with my pivoting to maximize my blows. This is where I see my LtRs pass harmlessly overhead. It's frustrating but with practice I can pretty reliably connect a LtR to a face. I practice this A LOT in the arena as the opponents will typically walk right into a LtR if you allow them to advance before initiating the attack.